Par trichard le 10 Janvier 2013 à 11:31
Everyday mobile tech takes the legwork out of tracking hard-to-find animals, and makes life easier for field biologists
Smile, you're on camera (Image: Ralph Clevenger/Corbis)
FIELD biology is notoriously laborious. In one famous 1982 study, Smithsonian entomologist Terry Erwin counted by hand the number of insect species in one hectare of forest canopy in Panama. By extrapolation Erwin estimated the total biodiversity of Earth's insects. What if your smartphone could take some of the strain?
Harvard biologist and computer scientist Walter Scheirer has devised a machine vision system that automatically recognises and counts specific animals and runs on a Motorola Droid X2 smartphone. This will help biologists make quicker, more accurate judgements about the health of delicate ecosystems.
Two years ago, Edwards Air Force Base in the Mojave desert, California, put out a call for a cheap way to monitor the animals that live there. The area is one of the last refuges for the endangered desert tortoises as well as the threatened Mojave ground squirrels (see map). Keeping an eye on the health of the animal population in such a remote location is time-consuming and expensive. So Scheirer developed detection and classification algorithms capable of identifying tortoises and squirrels with nothing more than a standard smartphone.
Automated camera traps already exist, but they are not selective enough. "Right now, we have to manually go through every photo to identify species and separate photos of interest from false photos. It's a very laborious task," says Princeton conservation biologist Siva Sundaresan, who works with Grévy's zebras in Kenya. He says Scheirer's method is potentially very useful to biologists.
But how does a phone tell the difference between a squirrel and a rock or a tumbleweed? Scheirer's system starts off by scanning its environment for objects that could be the animals it wants. It looks for clumps of pixels that are new to the scene, then examines them to decide whether they represent any of the animals it has been trained to recognise. Rather than checking each individual pixel, Scheirer's algorithms analyse the content of a frame of video and look for patterns of pixels that identify the animal. The algorithms don't need intensive processing and so run well on smartphones.
A paper due to be presented at the Workshop on the Applications of Computer Vision in Clearwater, Florida, later this month shows how well the algorithms work, with the system able to distinguish between three different species of ground squirrel 78 per cent of the time, even though they are almost identical. Scheirer says that the algorithms have been tweaked and that the recognition rate is now around 85 per cent.
Scheirer says his goal is to build a cheap, easy-to-use system that can automatically detect animals in any environment. More field trials are scheduled for next month, and the team aims to deliver a finished system to the US Air Force by 2014.
Princeton population biologist Dan Rubenstein says machine vision systems will also help us understand delicate ecosystems in finer detail. "You won't be generalising from such small scale to such a massive scale," he says. "We're going to be able to save ecosystems."
Another system presented at the conference, called Hotspotter, recognises individual animals like zebras and giraffes by their stripes and spots, although it still needs some human guidance, unlike the Mojave desert system. Rubenstein, who works on Hotspotter, says that systems like this will allow biologists to look at animals and their actions on an individual basis. "We could start to build massive databases of who's who, and how they move in time. We can use social networks to figure out how they relate to each other."
Par trichard le 27 Septembre 2012 à 21:57
Ocean Acidification Can Mess with a Fish's Mind
In more acidic waters clown fish wander too far from safety, sea snails fail to avoid prey
Monterey, Calif.—Mental problems at sea? Fish and mollusks could begin to have them—thanks to rising CO2 levels. Some of the resulting behaviors are odd, some compromising, and they reveal just how fundamentally carbon emissions are affecting our increasingly fragile Earth.
As humans emit more carbon dioxide into the atmosphere, more of the gas is absorbed by the oceans, gradually making the water more acidic. Numerous studies in recent years have documented how lower pH (higher acidity) can make it harder for shellfish and tiny organisms to form shells or internal skeletons and to reproduce. The acidity often forces the organisms to expend extra energy to counteract ill effects on their metabolisms as well. But now scientists are finding that lower pH can also mess with ocean animals' minds.
Small clown fish (yes, Nemo), for example, normally stay extremely close to the coral in which they spend their entire lives. But as the water becomes increasingly acidic—as in various recent experiments—they tend to wander farther and farther from home. This uncharacteristic "boldness" is not necessarily a good trait because the farther they swim, the more likely they are to get eaten by predators. Greater acidity also "impairs their ability to discriminate between the smell of kin and not, and of predators and not," according Philip Munday, a professor and research fellow at the Coral Reef Studies center at James Cook University in Australia, who conducted the experiments and presented results at a symposium here this week called The Ocean in a High-CO2 World.
Other species exhibit equally unusual behaviors. A snail known as Chilean abalone, which adheres to rocks along wave-swept shores, quickly rights and reattaches itself when it is dislodged, an important skill for avoiding predators. But when CO2 levels were raised by about 50 percent, some snails were slow to right themselves and others did not do so at all. "Their decision-making is delayed," said Patricio Manriquez, a researcher at the Southern University of Chile. Some snails took wrong turns in trying to avoid crab predators, and some even turned into the crab's claws instead of away from them.
In experiments done at the Monterey Bay Aquarium Research Institute here, hermit crabs living in highly acidic conditions did not show the increased boldness of Munday's clown fish, but they took far longer to withdraw into their shells than normal when they came under attack from a potential predator (in this case, a toy octopus).
Researchers are not sure what is causing the peculiar behaviors but Munday suspects that elevated CO2 levels interfere with a neurotransmitter called GABA, which plays a key role in modulating activity in the brain and nervous system of virtually all animals, including humans. In one experiment, Munday exposed reef fish to high CO2, which interfered with their sense of smell. He then administered a compound that helps to facilitate activity by receptors that sit on nerve cells and direct the cells' responses to GABA, and the abnormality was reversed. Because GABA is so ubiquitous, Munday fears that ocean acidification could cause sensory and behavioral problems for many sea creatures if global CO2 levels continue to rise.
Par trichard le 13 Juin 2012 à 11:25
WHO demands action on drug-resistant gonorrhoea
Staging a comeback (Image: CDC/Phanie/Rex Features)
Gonorrhoea, a sexually transmitted infection also known as "the clap", is making a comeback – and this time it may be incurable. New strains have emerged that resist the last few antibiotics that still worked against the disease.
In a rare public alert last week, the World Health Organization warned that highly resistant cases of gonorrhoea have now been detected in Japan, Europe and Australia. It is calling for a worldwide effort to track the superbug – and to develop new gonorrhoea drugs and vaccines.
That's a slim hope. Between the limited profits to be made from drugs that cure infections and the previous success of antibiotics against gonorrhoea, there has been little investment in the disease. "There are no new therapeutic drugs in development," says Manjula Lusti-Narasimhan of the WHO's Department of Reproductive Health and Research.
Yet epidemiological models show that the current official policies for managing gonorrhoea are virtually guaranteed to lead to a rebound in cases, and to antibiotic resistance.
Neisseria gonorrhoeae, also known as Gonococcus, infect an estimated 106 million people a year worldwide. The infection causes painful urination in men and can be symptomless in women, but left untreated it may cause painful pelvic inflammation and potentially fatal ectopic pregnancy. It can cause blindness in babies, and makes it easier to contract HIV.
It was among the first diseases to fall to antibiotics in the 1940s, but the bacteria readily acquire antibiotic resistance genes and keep them, even when the antibiotics they resist are no longer used. N. gonorrhoeae is now resistant to penicillin, and the subsequent families of antibiotics used to treat it.
Now only a couple of third-generation cephalosporin antibiotics are left. But resistance to these has been creeping up, and last year N. gonorrhoeae resistant enough to be dubbed a "superbug" was reported in Japan.
Most people clear the infection faster than they change sex partners, so don't spread the bug to someone new. But people who change partners faster, such as sex workers and promiscuous communities of men who have sex with men, are likely to pass on the infection. Targeting such groups for treatment caused gonorrhoea infection rates to drop steeply in industrialised countries since the 1970s – but now they are climbing again.
This could be because in models, treating these "core groups" is the only way to slash infection rates. But this is also an efficient way to select for antibiotic resistance, which then spreads widely. "It's a catch-22," says David Fisman of the University of Toronto, Canada.
Worse, the models show that relying on one drug until resistance builds up, then switching to another – precisely what health agencies have done – causes resistance fastest.
One way out might be diagnostic tests that reveal not just the strain of gonorrhoea responsible for infection, but which antibiotics it resists. Current DNA-based tests do not, meaning resistant infections are treated blindly, often with a drug that has no effect and can just worsen resistance. Fisman thinks this could be why gonorrhoea is increasing in some places.
The ultimate answer would be a gonorrhoea vaccine. Some efforts are underway, but have been unsuccessful – partly because the ancient disease is so well adapted to humans, people do not become immune even from repeated infections.
Par trichard le 30 Mai 2012 à 08:23
Polio Makes Its Last Stand
As global eradication efforts ramp up in Nigeria, Pakistan and Afghanistan, funding shortfalls threaten gains in Africa and Asia
May 28, 2012
By Ewen Callaway of Nature magazine
A hard-fought battle against the polio virus may be approaching its endgame. Last week, health officials laid out plans to eradicate the virus from its last redoubts, but warned that the effort may founder owing to a US$1-billion funding gap.
"We are truly at a tipping point in the program right now," says Bruce Aylward, an assistant director-general at the World Health Organization, who is leading the eradication effort. Speaking at the 65th World Health Assembly in Geneva, Switzerland, he announced an Emergency Action Plan to step up vaccination efforts in the three countries that have never been able to stop the virus from spreading: Nigeria, Afghanistan and Pakistan.
The plan, which would boost global spending to $2.2 billion over the next two years, aims to stamp out new polio cases by the end of this year. Some experts believe it will take longer, but they agree that the push will eventually deliver victory to the Global Polio Eradication Initiative (GPEI), a $9-billion campaign that began in 1988, a time when an estimated 350,000 people succumbed to polio each year. The initiative, based in Geneva, made rapid gains in the Americas, Europe and parts of Asia, but since 2001, incidence rates have plateaued, with 1,000-2,000 people developing poliomyelitis each year worldwide.
To eliminate those cases, the GPEI must ensure the vaccination of a majority of children in hard-to-reach and war-torn areas such as Kandahar province in Afghanistan. But the global economic crisis has created a $945-million gap of unfulfilled commitments in the initiative's budget for 2012-13, which is already forcing the campaign to limit vaccination in neighboring countries such as Niger and Tajikistan (see `Polio strongholds'). Although about one-third of that funding gap looks set to be filled, Aylward warned that shortfalls in the second half of this year could compel the GPEI to pull back in Afghanistan and Pakistan, too.
"If the money doesn't come and they can't build these walls of immunity, there is a risk that polio will implant itself and start circulating" in neighboring countries, says David Heymann, director of the Centre on Global Health Security at Chatham House in London, and former head of the WHO polio-eradication effort. China's western province of Xinjiang, for example, is fending off an outbreak that originated in Pakistan. The GPEI estimates that if polio is not eradicated and mass vaccination ceases, the number of children paralyzed each year will rise to 200,000 within a decade, and unvaccinated adults will be vulnerable to a more aggressive form of the disease, as they are in Xinjiang.
On 25 May the World Health Assembly passed a mostly symbolic measure declaring polio a "programmatic emergency for global public health", but progress in some countries has persuaded GPEI officials that eradication is within reach. India has not recorded a case of polio in 16 months: an unmitigated victory given that the country's high population density and poor hygiene has in the past made it ripe for the spread of the virus. A wide roll-out of new vaccines that effectively target the strains in circulation seems to have won the battle, says Nicholas Grassly, an epidemiologist at Imperial College London. India's success also shows that "the barriers are not technical, they are about management, implementation, oversight and commitment to eradicating polio", he adds.
Last year, Pakistan seemed to pose a major obstacle to eradication, not least because flooding in 2010 displaced millions of people, many of whom missed scheduled vaccinations. The program was also hampered by widespread suspicion after the revelation last July that the US Central Intelligence Agency may have used a vaccination campaign to obtain DNA from children living in Osama bin Laden's compound in Abbottabad (see Nature 475, 265; 2011). A doctor involved in that effort, Shakil Afridi, was last week sentenced to 33 years in prison.
The incident caused support for vaccination to plummet temporarily in Balochistan province and the Federally Administered Tribal Areas, where most of Pakistan's polio cases occurred last year, says Heidi Larson, an anthropologist at the London School of Hygiene and Tropical Medicine, who maintains a Vaccine Confidence Index for Pakistan and other developing countries.
But the country now seems to be making progress, recording just 16 cases of polio so far in 2012 -- half as many as this time last year, with none in Balochistan. In Afghanistan, worsening security led to a threefold increase in polio cases between 2010 and 2011, but the country has recorded just six cases so far this year. Nigeria, which registered 62 cases due to wild poliovirus strains in 2011 (as well as 33 cases caused by the spread of a strain used in the live vaccine), has had 35 cases so far this year.
The WHO's Emergency Action Plan includes measures tailored to individual areas, such as winning the support of Islamic scholars in Pakistan, and improving tracking of migrant populations in northern Nigeria. "It's a very ambitious program," says Zulfiqar Bhutta, an immunization expert at Aga Khan University in Karachi, Pakistan. But with a history of poor oversight and a lack of local accountability in the three remaining endemic countries, "the devil is in the detail of implementation".
However, India's success in staunching the spread of polio has shifted the discussion from whether polio will be fully eradicated, to when, says Aylward. The tentative deadline of the end of 2012 is likely to be the initiative's third missed goal, after deadlines in 2000 and 2005 passed the campaign by. "What's changed is that nobody is thinking, `Maybe we call it off'," says Aylward.